Conversion between CGmodel representation and PyRosetta Pose

[tlfobe]

We were working on getting the conversion between CG PyRosetta objects (Poses) and CGOpenMM/Foldamers (CGModel). This is important for being able to compare structures and energies from both codebases.

Garrett started this process in this branch of CG PyRosetta:
https://github.com/shirtsgroup/cg_pyrosetta/tree/cgopenmm_comparison/cg_pyrosetta

[tlfobe]

The difficulty here is the moving target of the PyRosetta representation of parameters.

Structures should be easy to port over, since the Pose object stores coordinates of a model. There was a question of consistency between atom names and residue names between both codebases. This was complicated by the CG11x3 residue needed to have torsions and bond angles apply correctly to the 1-1 model.

Where ideally each 1 bead/1 backbone residue would have the names of each atom in them (say BB1 and SC1), the current representation has 3 BB and 3 SC atoms per residue. This is different than the current representation of the 1-1 model in OpenMM.

The porting over of the energy functions would also be a bit weird. CG OpenMM has all the parameters defined at the beginning of a given simulation, where the goal with CG PyRosetta is to have parameters be in files and be read in from the command line when PyRosetta is run. Generating the correct energy parameter files for PyRosetta representation of the CGmodel seems straight forward, but would need some work.

Just my current thoughts on the matter, we can discuss more on the differences between model representations below.